loqusdb 2.7.21__tar.gz → 2.7.22__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (95) hide show
  1. {loqusdb-2.7.21 → loqusdb-2.7.22}/PKG-INFO +1 -1
  2. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/__init__.py +1 -1
  3. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/build_models/profile_variant.py +1 -1
  4. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/build_models/variant.py +2 -2
  5. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/commands/export.py +7 -3
  6. {loqusdb-2.7.21 → loqusdb-2.7.22}/pyproject.toml +1 -1
  7. {loqusdb-2.7.21 → loqusdb-2.7.22}/LICENSE +0 -0
  8. {loqusdb-2.7.21 → loqusdb-2.7.22}/README.md +0 -0
  9. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/__main__.py +0 -0
  10. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/build_models/__init__.py +0 -0
  11. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/build_models/case.py +0 -0
  12. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/commands/__init__.py +0 -0
  13. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/commands/annotate.py +0 -0
  14. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/commands/cli.py +0 -0
  15. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/commands/delete.py +0 -0
  16. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/commands/identity.py +0 -0
  17. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/commands/load.py +0 -0
  18. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/commands/load_profile.py +0 -0
  19. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/commands/migrate.py +0 -0
  20. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/commands/restore.py +0 -0
  21. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/commands/update.py +0 -0
  22. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/commands/view.py +0 -0
  23. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/commands/wipe.py +0 -0
  24. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/constants/__init__.py +0 -0
  25. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/exceptions/__init__.py +0 -0
  26. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/exceptions/case.py +0 -0
  27. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/exceptions/profile.py +0 -0
  28. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/exceptions/vcf.py +0 -0
  29. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/log.py +0 -0
  30. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/models/__init__.py +0 -0
  31. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/models/case.py +0 -0
  32. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/models/identity.py +0 -0
  33. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/models/profile_variant.py +0 -0
  34. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/models/variant.py +0 -0
  35. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/plugins/__init__.py +0 -0
  36. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/plugins/mongo/__init__.py +0 -0
  37. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/plugins/mongo/adapter.py +0 -0
  38. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/plugins/mongo/case.py +0 -0
  39. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/plugins/mongo/profile_variant.py +0 -0
  40. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/plugins/mongo/structural_variant.py +0 -0
  41. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/plugins/mongo/variant.py +0 -0
  42. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/resources/__init__.py +0 -0
  43. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/resources/loqusdb.20181005.gz +0 -0
  44. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/resources/maf_50_sites_GRCh37.vcf.gz +0 -0
  45. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/resources/maf_50_sites_GRCh38.vcf.gz +0 -0
  46. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/utils/__init__.py +0 -0
  47. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/utils/annotate.py +0 -0
  48. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/utils/case.py +0 -0
  49. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/utils/delete.py +0 -0
  50. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/utils/load.py +0 -0
  51. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/utils/migrate.py +0 -0
  52. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/utils/profiling.py +0 -0
  53. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/utils/update.py +0 -0
  54. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/utils/variant.py +0 -0
  55. {loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/utils/vcf.py +0 -0
  56. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/build_models/test_build_case.py +0 -0
  57. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/build_models/test_build_variant.py +0 -0
  58. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/build_models/test_is_greater.py +0 -0
  59. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/commands/test_export.py +0 -0
  60. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/commands/test_identity.py +0 -0
  61. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/commands/test_view.py +0 -0
  62. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/conftest.py +0 -0
  63. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/fixtures/643594.clinical.SV.vcf +0 -0
  64. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/fixtures/643594.clinical.vcf.gz +0 -0
  65. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/fixtures/double_variant.vcf +0 -0
  66. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/fixtures/funny_trio.ped +0 -0
  67. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/fixtures/profile_snv.vcf +0 -0
  68. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/fixtures/recessive_trio.ped +0 -0
  69. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/fixtures/test.SV.vcf +0 -0
  70. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/fixtures/test.vcf +0 -0
  71. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/fixtures/test.vcf.gz +0 -0
  72. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/fixtures/test.vcf.gz.tbi +0 -0
  73. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/fixtures/unsorted.vcf +0 -0
  74. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/functional/test_cli.py +0 -0
  75. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/plugins/mongo/test_case_operations.py +0 -0
  76. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/plugins/mongo/test_connect.py +0 -0
  77. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/plugins/mongo/test_flask_extension.py +0 -0
  78. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/plugins/mongo/test_get_sv.py +0 -0
  79. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/plugins/mongo/test_load_svs.py +0 -0
  80. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/plugins/mongo/test_variant_operations.py +0 -0
  81. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/utils/test_case.py +0 -0
  82. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/utils/test_delete.py +0 -0
  83. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/utils/test_delete_family.py +0 -0
  84. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/utils/test_delete_variant.py +0 -0
  85. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/utils/test_get_family.py +0 -0
  86. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/utils/test_load_database.py +0 -0
  87. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/utils/test_load_family.py +0 -0
  88. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/utils/test_load_variants.py +0 -0
  89. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/utils/test_migrate.py +0 -0
  90. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/utils/test_profiling.py +0 -0
  91. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/vcf_tools/test_check_par.py +0 -0
  92. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/vcf_tools/test_check_vcf.py +0 -0
  93. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/vcf_tools/test_format_sv_variant.py +0 -0
  94. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/vcf_tools/test_format_variant.py +0 -0
  95. {loqusdb-2.7.21 → loqusdb-2.7.22}/tests/vcf_tools/test_vcf.py +0 -0
{loqusdb-2.7.21 → loqusdb-2.7.22}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: loqusdb
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- Version: 2.7.21
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+ Version: 2.7.22
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  Summary: A simple observation count database
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  License: MIT
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  Author: Your Name
{loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/__init__.py RENAMED
@@ -4,7 +4,7 @@ from pymongo import ASCENDING, IndexModel
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  logger = logging.getLogger(__name__)
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- __version__ = "2.7.21"
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+ __version__ = "2.7.22"
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  INDEXES = {
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  "variant": [
{loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/build_models/profile_variant.py RENAMED
@@ -37,7 +37,7 @@ def build_profile_variant(variant, keep_chr_prefix=None):
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  chrom = variant.CHROM
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  if not keep_chr_prefix:
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- if chrom.startswith(("chr", "CHR", "Chr")):
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+ if chrom.lower().startswith("chr"):
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  chrom = chrom[3:]
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  pos = int(variant.POS)
{loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/build_models/variant.py RENAMED
@@ -99,7 +99,7 @@ def get_coords(variant, keep_chr_prefix, genome_build):
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  }
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  chrom = variant.CHROM
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  if not keep_chr_prefix:
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- if chrom.startswith(("chr", "CHR", "Chr")):
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+ if chrom.lower().startswith("chr"):
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  chrom = chrom[3:]
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  coordinates["chrom"] = chrom
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  end_chrom = chrom
@@ -121,7 +121,7 @@ def get_coords(variant, keep_chr_prefix, genome_build):
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  other_coordinates = alt.strip("ATCGN").strip("[]").split(":")
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  end_chrom = other_coordinates[0]
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  if not keep_chr_prefix:
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- if end_chrom.startswith(("chr", "CHR", "Chr")):
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+ if chrom.lower().startswith("chr"):
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  end_chrom = end_chrom[3:]
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  end = int(other_coordinates[1])
{loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/commands/export.py RENAMED
@@ -56,9 +56,13 @@ def export(ctx, outfile, variant_type, freq):
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  if genome == GRCH37 and chrom in existing_chromosomes:
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  ordered_chromosomes.append(chrom)
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  existing_chromosomes.remove(chrom)
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- elif genome == GRCH38 and chrom[3:] in existing_chromosomes:
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- ordered_chromosomes.append(chrom)
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- existing_chromosomes.remove(chrom)
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+ elif genome == GRCH38:
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+ if chrom[3:] in existing_chromosomes:
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+ ordered_chromosomes.append(chrom[3:])
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+ existing_chromosomes.remove(chrom[3:])
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+ elif chrom in existing_chromosomes:
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+ ordered_chromosomes.append(chrom)
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+ existing_chromosomes.remove(chrom)
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  for chrom in existing_chromosomes:
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  ordered_chromosomes.append(chrom)
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{loqusdb-2.7.21 → loqusdb-2.7.22}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "loqusdb"
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- version = "2.7.21"
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+ version = "2.7.22"
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  description = "A simple observation count database"
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  authors = ["Your Name <you@example.com>"]
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  license = "MIT"
{loqusdb-2.7.21 → loqusdb-2.7.22}/LICENSE RENAMED
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{loqusdb-2.7.21 → loqusdb-2.7.22}/README.md RENAMED
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{loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/__main__.py RENAMED
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{loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/log.py RENAMED
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{loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/utils/case.py RENAMED
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{loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/utils/load.py RENAMED
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{loqusdb-2.7.21 → loqusdb-2.7.22}/loqusdb/utils/vcf.py RENAMED
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{loqusdb-2.7.21 → loqusdb-2.7.22}/tests/conftest.py RENAMED
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